8- A Closer Look at the Core


Essay 1 provided a non-technical overview of the brain’s reticular core.  Written for non-scientists, it simplified or oversimplified various neurological complexities.

For those wanting more detail and clarity, this essay takes a closer look.  It might serve as a bridge to other articles and books about the brain.  There are many good ones out there, supposedly written at least in part for non-scientists.  They address all kinds of interesting issues, but most are daunting in their complexity and use of technical terms.  This may help with that.

Along the way, we’ll look more closely at some basic psychological and spiritual questions.


To begin, the reticular system is not just a tangle of diffuse neural networks.  Within its networks are also some more distinct pathways  (nuclei = clumps of neurons organized as small processing centers, and the tracts interconnecting them).  Most reticular nuclei and tracts are more loosely organized than those of other brain regions.  They overlap, with unclear boundaries and diffuse interconnections, and all tend to merge with surrounding core networks.  Nevertheless, they do have some semi-distinct structure and connection patterns.

The more organized and easily identifiable reticular pathways were natural starting points for researchers trying to untangle that labyrinth.  The mapping process started about a century ago, went slowly at first, then rapidly gained speed as new research techniques were developed.  Today over two hundred reticular nuclei and tracts have been identified and named.

The Glossary section describes some of them.  But the rest of this essay avoids technical terms and descriptions.  Here “reticular networks” still includes core nuclei, tracts, and the networks in which they are embedded.

Research has become so focused on specific core pathways, including their neurotransmitter chemistries and likely functional roles, that the “reticular” label is now used mostly as an umbrella term, referring loosely to all core regions.  Some feel it’s too general, too imprecise given our current knowledge, and that its use should be dropped.  But the need for an umbrella term remains.  Terms like “subcortical midline systems”, “centromedian brainstem structures”, and “core arousal networks” are sometimes used instead, but most still use the familiar “reticular” term.  Again quoting neurologist Adam Zeman  –  “the concept captures important truths…It remains an enlightening simplification.”


Core Consciousness

So does your brain’s ancient core generate its own primal awareness?

That question, once considered scientific heresy, is increasingly answered  “probably yes.”  And most would agree it has these two basic features:

It’s primarily visceral.  Core networks are the primary regulators of internal body functions, including visceral sensations.  Other core functions are intimately interwoven with its visceral functions.

And it’s largely undifferentiated.  Core awareness is most basically undifferentiated visceral awareness.

We’re usually not aware of our internal organs.  Visceral perception is much less keen than external perception, like vision or hearing.  When internal needs arise, sensations like hunger or bladder fullness direct our attention to them, but visceral perception is mostly subliminal.  It is diffuse, undifferentiated, often just at the edge of awareness.  That’s largely due to reticular processing patterns.

A possible source of confusion here is the paradoxical combination of specificity and diffuseness in reticular processing.  On one hand, core nuclei contain more or less organized micro-circuits, which regulate distinct visceral functions.  Examples include breathing, heart rate, digestion, and hormone levels.  In this regard, reticular processing is fairly specific. On the other hand, those core nuclei are embedded in diffuse core networks, which mix and merge signals from many sources.  They enable crosstalk and signal spillover among core nuclei.  And the brain’s core is particularly sensitive to hormones and neuropeptide chemicals, which further bias and blur processing.  So we have this paradox  —  mostly differentiated visceral regulation and mostly undifferentiated visceral perception.

Reticular networks not only process signals from internal organs, but from all brain regions as well.  These flow, mix, and blend with visceral signals, amplifying the non-specific flux of core processing.

This fluid core processing underlies what neurologist Antonio Damasio calls “primordial feeling”  —  the basic stuff of core consciousness.  It results from “richly mixing signals from the body” in core networks.  He says “rather than mere slavish maps of the body,” primordial feelings are “devoid of spatial detail.”  They are diffuse feelings of simple being.

These feelings are the essence of Damasio’s core self.   Here is a simple “sense of self-knowing,”  an awareness “of your own existence.”  Such awareness changes little over time  —  it’s “approximately the same whether you are three years old or fifty or eighty.”  So it gives the self a sense of continuity over time.  He calls it the “stable platform” or “core of sameness” running through other “ingredients of the self.”

This important but potentially confusing point bears repeating.  Reticular input comes mostly from the body, especially visceral organs, but we usually perceive it as undifferentiated being.  Within core networks, input signals lose much of their specific information value.  According to Damasio,  there is no clear body image or specific awareness of internal organs.  Instead, there’s a sense of “sheer existence,” a “wordless affirmation that I am alive.”

So again, core consciousness is basically undifferentiated visceral awareness.  Damasio says

“I call it primordial feeling, and I note that it has a definite quality, a valence, somewhere along the pleasure-to-pain range.  It is the primitive behind all feelings of emotion and therefore is the basis of all feelings.”

Core awareness, he says, has emotional valence  —  “somewhere along the pleasure-to-pain range” —


Positive and Negative Core Networks

Pleasure and pain are programmed in complex neural networks throughout the brain’s core.  These networks are roughly equivalent to the classic “reward” and “punishment” systems, with which you may be familiar.  Stimulation of them in humans, using implanted electrodes or drugs, produces intense positive or negative feelings.  Stimulation of the same networks in animals produces similarly intense approach or avoidance behaviors.

Let’s look first at the positive networks  –

As outlined in Essay 4, they form the core of positive emotion systems on each brain level.  In the brainstem, we have instinctive pleasure-approach drives like eating and sex.  On the limbic level, we have social caring and bonding emotions.    On the cortical level, we have positive thought patterns like wishes, goals, and values.  But at the core of all positive emotions  —  brainstem, limbic, and cortical  —  are reticular “pleasure centers.”

That has been the common view of the brain’s reward system.  Multiple pleasure centers, diffusely interconnected in a web of core networks, activate all positive emotions.  Some turn on when we eat a good meal, others when we enjoy a friendly visit or appreciate fine art.  That positive core, with its interconnected senses of pleasure, has been called a “river of reward.”

And that view is roughly accurate, as far as it goes.  But it leaves out an important part of the reward system  —

That part has been called the “anticipatory” or “seeking” reward system.  It’s not active during the experience of pleasure, but before that, in the anticipation or search for pleasure.  Yet the anticipation is in itself rewarding.

Psychobiologist Jaak Panksepp researched and wrote extensively about this system, which he called the SEEKING system.  Here is his description:

“Even though there are many reward systems in the brain, there is only one that drives the animal energetically to seek all the other kinds of rewards.”

“[All] the other emotions also rely upon the psychobehavioral push of the SEEKING urge.  In a sense, SEEKING is the ‘granddaddy’ of all the emotion systems.”

“Arousal of this SEEKING system produces all kinds of approach behaviors, but it also feels good in a special way.”

This is thought to be one of the first systems that evolved in primitive vertebrates’ brains.  We don’t know most details of its interactions with other reward systems, but many researchers point to its non-specific activating role.       It has been called a “central trunk line” activating many systems throughout the brain. Panksepp called it a “remarkable general-purpose system that is designed for SEEKING anything and everything.”

“[The] SEEKING system generates energetic exploration and foraging…the feeling is one of anticipatory-expectant eagerness…These are feelings that lie at the very heart of what some might call joyous aliveness.”

“With [SEEKING system] stimulation, animals appear enthused and are keen to explore their environments.  And people accordingly feel more interested in the world and make future plans – clearly a state of high-hearted expectation…[This] arousal generates a reward that is closer to euphoria than to any sensory-bodily pleasure.”

Intense excitement and euphoria occur when the system is artificially stimulated by electrodes or drugs.  But as Panksepp said, it usually “operates more or less continuously in the background, albeit at much lower levels.”  It’s usually experienced as vigor, interest, or happiness.  It generates a sense of well-being and “keeps us in a general state of engagement with the world.”

Finally, recall from Essay 1 that reticular networks respond selectively to anything new.  As Panksepp pointed out, “the SEEKING system is also briefly aroused by all novel events [or] changes in the environment.”  It “prompts us to satisfy our liking for novelty.”

And now a look at negative core networks  —

Sometimes called the brain’s “punishment system,”  it  —  like the reward system  —  has networks throughout the core.  Stimulating them elicits intense negative responses in humans and other animals. They form the core of negative emotion systems at each brain level.

At the brainstem level, physical pain pathways are closely tied in with instinctive programs for fight and flight.  Other brainstem pathways mediate other unpleasant sensations like bad tastes, nausea, and air hunger.  Limbic pathways underlie negative social emotions  —  social aggression and anxiety, the emotional pain of separation and loss.  The cerebral cortex elaborates cognitive versions of them all  —  critical, worrisome, or pessimistic thought patterns.

Of course, all those negative emotions are rooted in reticular networks.  Pain, fear, anger, disgust, shame, jealousy, worry  —  all physical, emotional, and cognitive pain/displeasure  —  their roots are entangled in core networks.

Are the roots of those specific negative emotions entangled in a non-specific “central trunk line,” similar to the SEEKING system of positive emotion?   If so, does that diffuse negative core generate some poorly differentiated sense of pain or angst?  Or do negative core networks just contain the mixed roots of separate and distinct painful emotions?  There’s currently a debate about that.  Some combination of both views is likely accurate.

Negative networks are also intertwined with positive networks.  Some reticular regions contain positive networks only, others negative only, but in many regions they overlap.  Behavioral biologist James Olds described an early (1950’s) electrode stimulation experiment:

“In a large intermediate area there was an obvious mixture of positive and negative effects…There was no amount of stimulation in these areas that seemed just right.  The animal behaved as if it could not stand the stimulation but could not resist it either.”

By the mid-1970’s, researchers had developed some good rough maps of core emotion systems.  According to Olds

“Rats, cats and monkeys had much the same map.  Even humans would perform nonsense tasks apparently in order to stimulate analogous brain centers, although they often seemed confused as to why they were doing so.”

In recent decades, our maps have of course gotten much better.      But the more we learn, the more we realize how much we still don’t know.

What we do know is that all our complex emotions, and all their dynamic interactions on brainstem, limbic, and cortical levels, are rooted in reticular networks.  As Damasio says, “All feelings of emotion are complex musical variations on primordial feelings.”

Here are your deepest emotions, positive and negative, the yin and yang at the core of your being.


Three Key Brainstem Regions

Brainstem and its core

As outlined in Essay 1, the reticular system runs lengthwise through the center of the brainstem.  At its upper end it splits in two major branches, one projecting diffusely throughout the limbic system, the other throughout the cerebral cortex.  Another branch projects similarly to the cerebellum.

To that basic overview model, we now add three important brainstem regions  –

The hypothalamus and thalamus are most closely related to the limbic system and cerebral cortex respectively. The vestibular nuclei are most closely related to the cerebellum.

Here’s a brief overview of their major functions, and a closer look at their relations with the core.



Visceral and hormonal regulation  –  The  hypothalamus regulates heart rate, blood pressure, respiration, thirst, appetite, digestion, bowel and bladder functions, sexual drives, and other body functions.  Those are also regulated in the lower brainstem core, but the hypothalamus plays a master role in orchestrating them all.  It also directly or indirectly governs all hormone-producing glands.  Growth hormone, thyroid, parathyroid, testosterone, estrogen, cortisol, other steroids  –  the hypothalamus regulates body chemistry as well as body organs.

 Limbic regulation  –  It has strong two-way connections with all limbic regions, and is central to all limbic functions.  Some writers refer to the limbic system as the hypothalamic-limbic system.  So the hypothalamus is an overlap region, part of both the brainstem and limbic system.  It’s the major focal point of brainstem-limbic interactions.

In humans, the hypothalamus is about the size of a pea.  Scientists often comment on the many complex functions this small region performs.  For example, physiological psychologist Simon Green:

“The hypothalamus…consists of some hundreds of thousands of neurons, i.e. a small number in comparison with the billions of neurons in the cerebellum and neocortex.  It is therefore an excellent example of the processing power of brain tissue.”

The hypothalamus contains hundreds of thousands of neurons.  Many are in semi-distinct nuclei, which regulate specific visceral and limbic functions.  But many are in diffuse networks, part of the reticular core  —

As the diagram indicates, a major reticular branch enters the hypothalamus.  In some places, it courses directly through, but in many places it intertwines among specific nuclei.  In fact, the hypothalamus itself is often considered a highly specialized part of the reticular system.

From the hypothalamus, reticular networks project diffusely throughout the limbic system.  Hypothalamic networks have been called “the activating core of emotion” and “the hub of the limbic wheel.”  They activate and deactivate limbic pathways in changing emotional patterns.

You may recall from Essay 1 that neurophysiologist  J.Z. Young was among the first scientists to speculate about possible reticular consciousness.   “Those life-promoting activities of the hypothalamus and reticular system,” he said, “are at the centre of all consciousness.”



Perceptual processing  –  Most external sensory stimuli (vision, hearing, etc) are first processed in the lower brainstem, then relayed to the thalamus, which puts them all together in simple perceptual patterns.  It’s the highest level of sensory processing in a reptile’s brain. In humans, the cerebral cortex expands perceptual processing, and confers new conceptual skills, but it still functions closely together with the thalamus.

“Gateway to the cortex”  –  Almost all information reaching the cortex is routed through the thalamus.  Many large pathways interconnect the cortex and thalamus, and they function together as one system  –  the thalamocortical system.  The thalamus is central to all cortical processing.

A major reticular branch projects into the thalamus, and from there throughout the cerebral cortex.  Within the thalamus, reticular networks make up its central core.  In addition, numerous reticular networks are intermingled among the specific (mostly perceptual) thalamic nuclei.

Those various networks are mostly activating.  Some project to limited cortical areas, and are thought to underlie selective attention functions.  Others project diffusely throughout the cortex, and probably activate global awareness patterns.

Another set of reticular networks is mostly inhibitory.  They form a net-like sheath around most of the thalamus, monitoring and controlling all signal traffic between it and the cortex.  They are important in the global deactivation of sleep, and in the inhibitory filtering functions of attention.

So all together these activating and inhibiting reticular networks form the functional core of the thalamocortical system.  They activate and deactivate it, waking the cortex and putting it to sleep.  They register perceptions and regulate thought patterns.  Here’s the conscious core of  intelligence.  Neurophysiologist Arnold Scheibel again —  “Perhaps here resides our source of knowing, and of knowing that we know.”


Vestibular Nuclei

The vestibular nuclei are strongly connected with the cerebellum.  They function closely together with it as the vestibulocerebellar system.

Vestibular nuclei receive their main input from inner ear balance sensors. They underlie our sense of balance, and regulate reflex “righting responses”  –movement adjustments that keep the body balanced.  They have similar integrating/orienting influences on sensory functions, and similar stabilizing influences on visceral functions.

So while it’s roughly accurate to call the cerebellum our “balance system,”  that term best applies to the vestibulocerebellar system as a whole.

As noted in Essay 4, the reticular networks that project to the cerebellum are described as “separate and distinct from the major reticular formation.”  They are easily distinguished from other core networks, which in contrast “grade almost imperceptibly from one to another.”

Why this anatomical separation of pre-cerebellar reticular networks from other reticular networks?  It probably reflects major functional differences between the brain’s emotion and balance systems, and in particular, between core networks related to emotion and those related to balance.

Most of the core contains interwoven positive and negative networks, which activate positive and negative emotion systems throughout the brain.  The separate pre-cerebellar networks activate the cerebellum, which provides a third force, a neutral, non-emotional balance force.  Those three forces  —  positive, negative, and balance  —  interact continuously on all brain levels, as outlined in Essay 4.


We’ll return to core brain anatomy in the Glossary section.


A River Runs Through It

“Let us look, then, inside our conscious minds and try to observe what the mind is like…To begin with, down at the bottom, the simple conscious mind is not unlike what William James described as a flowing stream with objects in it.”

                                                                                                                                                   – Neurologist Antonio Damasio

Damasio doesn’t elaborate on James’ stream-of-consciousness metaphor, but James’ meaning is clear.  The stream is pure consciousness itself.  It flows in our inner depths, carrying “objects” — specific perceptions, images, thoughts, feelings — along with it.

James maintained that psychologists, discussing the stream of consciousness, often mistake the objects for the stream.  They seem to be unaware of the underlying “free water of consciousness” in which those objects flow.  The stream, he said, is actually our spiritual core  —  “The spiritual self is no other than the stream of consciousness itself.”   It is “felt by all men as a sort of innermost center.”

Carl Jung recognized that underground river theme in the dreams of patients who were engaged in personal growth.  Such images symbolize, he said, unconscious spiritual life.

“Water is the commonest symbol for the unconscious…which lies, as it were, underneath consciousness.”

In subsequent dreams, with spiritual growth and individuation, the river may break through, flowing above ground in clear springs and fountains of conscious life.

Rivers are common metaphors in most religions.  In Jewish mysticism, according to Rabbi Lawrence Kushner, your soul is an underground river  —   “a sacred stream, luminous and ubiquitous, a River of Light.”

We can grow, he says, by “allowing the river of light  —  the deepest currents of consciousness  —  to rise to the surface and…animate our lives.”

Similar images occur in both Old and New Testaments.   For example:

“…the river of the water of life, as clear as crystal, flowing from the throne of God.”

“Whoever believes in me, as the Scripture has said, rivers of living water will flow from within them.”

The Christian baptism is a symbolic immersion in those waters.

In the Koran, gardens are prominent symbols of spiritually fulfilled lives.    It refers more than 30 times to “gardens beneath which rivers flow.”  Paradise itself is such a garden  –

“The parable of the Garden which the righteous are promised! – Beneath it flow rivers, perpetual is the enjoyment.”

In Buddhism, the seeker

“aspires to drink from the fountain of life itself instead of merely listening to remarks about it.  [He] is not satisfied until he scoops with his own hands the living waters of Reality, which alone, as he knows, will quench his thirst.”

                                                                                                                                                     — Zen scholar D.T. Suzuki

The Buddhist novice, starting out in search of enlightenment, is said to be  “one who has entered the stream.”

In Hinduism, rivers have similar spiritual resonance, and are traditionally honored as sacred.  And one of Hinduism’s most prominent symbols is the river-ocean metaphor  —  “Just as the river flows into the ocean, so the soul will unite with God.”


Into the Ocean?

Do our souls really unite with God, with a universal ocean of consciousness?

Well, modern physics does tell us that the universe is an ocean of energy fields, and that it may be conscious.  Not that it is conscious, but that it may well be conscious.

Classical physics told us there are four basic physical realities:  space, time, matter, and energy.  But modern physics has shown that space, time, and matter are all basically illusions, just ways we perceive the underlying energy fields.  Everything is energy.  The universe is an infinite ocean of interpenetrating and interacting energy fields.

Essay 6 introduced other findings of modern physics, which further prove, beyond any doubt, that our usual commonsense views of reality are wildly inaccurate.  Those findings don’t prove the existence of paranormal or spiritual phenomena, but they do suggest that such things may be real.  There was no room for magic in classical physics, but there may be in modern physics.

Essay 7 reviewed possible answers to the mind-body question.  It focused particularly on panpsychism, which fits well with both neuroscience and modern physics, and so has seen a corresponding increase in scientific credibility.  As a form of identity theory, it’s fully compatible with neuroscience.  And as modern physics changed our worldviews to reflect seemingly bizarre basic realities, panpsychism also seems to fit with them.  It no longer seems far-fetched.

Panpsychism maintains that all physical energies have mental aspects, and all mental energies have physical aspects.  So consciousness is present in brains and everywhere else.  Brains just amplify and refine that consciousness, which has always been present throughout the universe. We’re not isolated islands of consciousness in a mostly lifeless universe, but interconnected souls in an ocean of conscious life.

We went over all that in previous essays.  Here we’ll just focus briefly on the fundamental force field, from which all other energy fields emanate  —

Ground state energy, unified field, zero point field, quantum vacuum energy  –  these terms all apply loosely to the fundamental force field of physics.  We now know it’s present everywhere, even in what we used to call “empty space.”   Even a total vacuum contains this constantly fluctuating ground energy.  It has been called a “roiling sea,” from which energy radiates and subatomic particles pop into and out of existence.  It’s thought by some to be intensely energetic  —  “buzzing with its own strange energy”  —  and packed with dynamic potential.

But by other calculations, its “energy density” is much lower than that.  The roiling sea is more tranquil, fluctuates gently, still dynamic but less intense.  Other physicists think its energy density may be variable.

So we know it exists, but its true nature remains mostly a mystery.  Understanding the quantum vacuum has become a central challenge for modern physics.

And a central question is whether it is conscious.  Of course, there’s no proof either way.  But the findings of modern physics lead many scientists, especially quantum physicists, to embrace at least the possibility of a conscious universe.

If that fundamental force field, sometimes called the unified field, is actually conscious, then it must also be what various religions call holy spirit  (“holy” means unified or whole).   Of course, that’s the central theme of an emerging spiritual/scentific worldview.  If interested, you can google “consciousness” or “spirituality” plus any of those “ground state energy” terms listed above.

Some say this new science “promises to give us back our optimism.” It provides hope that our souls, one way or another, may survive in a living, conscious universe.  It doesn’t eliminate the need for faith, but does make that faith easier.

“We physicists are the only scientists who can say the word ‘God’ and not blush.”

                                                                                                  — Physicist Michio Kaku

“The first gulp from the glass of natural sciences will make you an atheist, but at the bottom of the glass God is waiting.”

                                                                                                                         — Physicist Werner Heisenberg

“Instead of proving that God doesn’t exist, maybe science will broaden our definition of divinity.”

                                                                                                                  — Science writer Mark Alpert

Scientists who “broaden our definition of divinity”  –  Albert Einstein is the classic example.  He rejected traditional dualist views of God, but often wrote and spoke about his “deep religious feelings.”  He endorsed panpsychism, and the mysticism it implies. Most of his scientific work focused on unified field theory, and he embraced a corresponding unitarian view of God  —

“A human being is part of the whole, called by us the ‘Universe’… He experiences himself, his thoughts and feelings as something separate from the rest – a kind of optical illusion of his consciousness. This delusion is a kind of prison for us.”

The illusion of separateness is based on our sense of space and time, which science tells us are both basically illusions.  The universe and all its physical/mental energy fields are actually an “undissectable whole.”

Another great physicist, Erwin Schroedinger, put it this way:

“Mind is by its very nature a singular tantum.  I should say:  the overall number of minds is just one.  I venture to call it indestructible since it has a peculiar timetable, namely mind is always now…I am now talking religion, not science —  a religion, however, not opposed to science, but supported by what disinterested science has brought to the fore.”

And as Einstein said, there is “a path to liberation” from those illusions, and a “foundation for inner security” —

“The most beautiful emotion we can experience is the mystical. It is the sower of all true art and science. He to whom this emotion is a stranger…is as good as dead.  To know that what is impenetrable to us really exists, manifesting itself as the highest wisdom and most radiant beauty…this knowledge, this feeling, is at the heart of true religiousness.”


We’ll return to these considerations after the Glossary.


Core Brain Glossary

You might want to use this Glossary as a reference, a springboard for further reading, or just for skimming.

As noted earlier, there are plenty of brain books and websites, full of interesting facts and insights, addressed at least in part to non-scientists.  If you decide to explore some of them, but find yourself bogged down by the often dense terminology, this might help.

So as a reference, or just for skimming, here’s an overview of some well-known reticular regions, starting with its major divisions  —

Brainstem and its core major divisions

The brainstem can be divided into medullary, pontine, midbrain, and upper brainstem (or diencephalic) regions.  Its reticular core is divided into those same four parts.

Some authorities don’t classify the diencephalon as part of the brainstem.  They consider the midbrain to be “upper brainstem.”

In most of the brain, including the brainstem, right and left sides are duplicated as mirror images of each other.  While we usually speak of them as singular, we have two of most brain systems or structures.  That holds for some parts of the reticular core as well.  But some parts are actually in the midline, and so are not duplicated.

The non-reticular or specific regions of the brainstem contain distinct sensory and motor pathways, precisely organized in many micro-systems.  They underlie simple sensory-motor reflexes and complex instinctive behavior patterns.

But at the core of that specific micro-circuitry are the more diffuse reticular networks.  Again, neuroanatomist David Bowsher describes a typical brainstem nucleus:

“[It] shows a clear-cut peripheral margin, but internally appears to merge with the reticular core…there is no clear internal boundary…It is as though the specific nuclei on the edge of the reticular core had been dragged away from it and differentiated out of it.”

Within the core networks, at each of the four brainstem levels, are various “reticular nuclei”  –  clusters or clumps of neurons, somewhat organized, but not to the same degree as specific nuclei elsewhere in the brain. Looking like tangled knots in the networks, they are actually functional nodes.

Each reticular nucleus plays its own role, or combination of roles, in sleeping, waking, arousal, attention, visceral, emotional, motor, or sensory functions.  But they all blend together in the fluid processing patterns of core networks.


Medullary Reticular Formation

Extends downward into spinal cord and upward into pons.

Most of it has a pronounced three-dimensional netlike appearance, described in terms like “fields” and “zones” and “clusters” of neurons.  It’s nuclei are also loosely organized.  Here are a few of them  –

Raphe nuclei  –  mostly small clusters of neurons, forming a loosely connected chain of nuclei, which extends through the center of medulla, pons, and midbrain.  Has been described as “the most medial [central] part of the brainstem.”

Project diffusely throughout the brain, use serotonin as their main neurotransmitter.  Contain over 85% of the brain’s serotonergic neurons.

(One way core networks are mapped is by identifying their neurotransmitter chemicals.  Most reticular nuclei use multiple neurotransmitters, but a few use one so exclusively that it’s considered a distinguishing feature.)

Best-known roles are waking activation, mood regulation, and pain processing.   But also participate in many other still poorly understood core functions.  Neuropsychologist Marc Dingman describes it this way  –

“The projections from the raphe nuclei are pervasive, carrying serotonin throughout the central nervous system. Thus, the functions that can be linked back to the raphe nuclei are also extensive and complex… These neurons are highly active during wakefulness, but are less active during sleep  –  and almost completely inactive during REM sleep.”

 Solitary Nucleus (or nucleus tractus solitarius)  –  an important visceral processing center, especially visceral sensory processing.   Receives input from cardiovascular, respiratory, gastrointestinal, and other internal body organs.  Also receives sensory input from taste receptors in mouth and tongue.

Neurologist Antonio Damasio envisions it as a likely source of core consciousness. Here all kinds of visceral sensations converge, blend, and are experienced together as primordial feelings, which he says “constitute the very first and inchoate revelation, to the mind, that its organism is alive.”

Gigantocellular Nucleus  –  an extensive network of very large (“giant “) neurons in the medullary core.  Loosely organized and distinguished as a nucleus mostly by the size of its neurons.  Acetylcholine is its main neurotransmitter.  Has wide range of poorly understood visceral and motor functions.  Has activating influences on both waking and dreaming awareness.

Pre-Cerebellar Reticular Nuclei  –  located in medulla and pons, project to cerebellum.  Most prominent are lateral reticular nucleus, tegmental pontine reticular nucleus, and paramedian reticular nucleus.  As noted previously, they are mostly distinct from other reticular networks.

The vestibular nuclei, so closely related to the cerebellum, are not part of the reticular formation.  But they are strongly interconnected with reticular nuclei throughout the core.


Pontine Reticular Formation

An upward extension of the medullary core, it has the same weblike organization, in which various reticular nuclei are embedded.

Locus Ceruleus  –  has widely divergent connections with all brain regions.  Norepinephrine (aka noradrenalin) is its primary neurotransmitter.

Not directly involved in sleep-wake regulation, but plays prominent activating role in response to novel or emotionally charged stimuli  –  positive and negative.  In that way, it does promote wakefulness.

Otherwise its influences are widely dispersed and mostly described as “intractable to full characterization” or simply as “elusive.”  But we do have a few pieces of the puzzle.  For example, the pontine micturation center, a network associated with the locus ceruleus, participates in bladder regulation.  It functions together with urinary control centers at multiple brain and spinal levels.

Parabrachial nucleus  –  strongly interconnected with the solitary nucleus (in the medulla, described above).  Both process visceral sensory input, and neurologist Damasio suggests they work together as generators of core consciousness.

“The circumstantial evidence in favor of this idea is telling. The nucleus tractus solitarius and the parabrachial nucleus receive a full complement of signals describing the state of the internal milieu in the entire body. Nothing escapes them…The signals compose a comprehensive picture of the internal milieu and viscera, and that picture happens to be the prime component of our feeling states.”

And it recently became clear that these two nuclei, through connections with other reticular nuclei, help activate the cerebral cortex.  This further supports the long-held view that

“cortical activation is not likely to depend on one single brainstem nucleus or one single family of nuclei but rather on a network formed by several families of nuclei.”

                                                                                                                          – Neurologists Josef Parvizi and Antonio Damasio

 Pontine Reticular Nucleus – Caudalis and Oralis  –  an upward extension of medullary giganticocellular nucleus.  Plays key role in dream or REM sleep  –  activates rapid eye movements, decreases muscle tone, decreases most cortical activity, but promotes dream imagery.

Also has various positive and negative motor and visceral functions, like eating drives and acoustic startle reflex.

 Pedunculopontine Nucleus  –  located in pons and midbrain.  Most prominent roles are motor decision-making and promotion of activated states in both waking and dream sleep.


Midbrain Reticular Formation

Also called mesencephalic reticular formation.  Extends downward into pontine core, and upward in two major branches to hypothalamus and thalamus. A few small projections bypass both of those, going directly to limbic system or cerebral cortex.

The midbrain core is more densely packed with nuclei than the medullary and pontine portions, but has the same basic network structure.

Deep Mesencephalic Nucleus  –  an upward extension of that same basic network structure of pons and medulla.  But it’s surrounded by, and interconnected with, more highly organized midbrain reticular nuclei.  It promotes fast, efficient, and fluid interactions among them.

Input signals to this nucleus are said to “arise from diverse areas of the brain” then blend together as they “distribute throughout the entire extent of the deep mesencephalic nucleus.”  Probably involved in most reticular functions.

Periaqueductal Gray (or PAG, also “central gray”)  –  a central crossroads for all  emotions  –  not only those of the brainstem, but also those on limbic and cortical levels.

Psychobiologist Jaak Panksepp called it “the most ancient, and most highly concentrated, emotional convergence zone within the brain”  —

“All aspects of consciousness emerge in animal and human brains as a result of the interactions of widespread neuronal networks. There is no single circuit or “center” for consciousness, even though there are critical convergence points.    As I have long argued, the PAG may be the most important…because it is richly connected to both higher and lower brain functions. It is a Grand Central Station for our affective life, and it is essential for the primal integration of diverse emotional experiences. It extends its tentacles far into the lower and higher regions of the brain.”

Neurologist Damasio agrees.  He calls the PAG a “pivotal link” in the “resonant loop” of core consciousness.  The PAG, together with solitary nucleus and parabrachial nucleus (both described above), generate primordial feelings  –  the essence of core consciousness.

The PAG is organized into “discrete functional subregions”  –  interconnected clusters of neurons involved in many aspects of positive and negative emotion.    So it’s no surprise that well over a dozen chemical neurotransmitters play significant roles in PAG processing.

Ventral Tegmental Area  –  a midbrain pleasure center, an important node in positive core networks, part of the brain’s reward system.  Dopamine is its main neurotransmitter.  Has diverse connections within brainstem and strong connections with hypothalamic-limbic system.

Recently found to contain some smaller networks related to “aversive stimuli”  –  an example of positive-negative system overlap found throughout the core.

Substantia Nigra  –  partially overlaps with the ventral tegmental area (above). Dopamine is also its main neurotransmitter.  These are the brain’s two major dopaminergic systems.

Has primarily motor functions, especially in selection of particular actions from various options.  Also plays poorly understood role in REM or dream sleep.

Midbrain Locomotor Region  –  upward extension of pedopeduncular nucleus (described above).  Participates in gross emotional movement patterns, like walking or running toward positive or away from negative stimuli.   Has activating influence in waking and in dream sleep.

Red Nucleus (or nucleus ruber)  –  another motor nucleus, controls limb movements, including reaching and grasping.

Part of it has a reticular organization, and in some places it blends with the core.   A larger part is more organized, with distinct boundaries and connections.  But the whole thing lies within the midbrain core.  So some scientists consider it part of the reticular formation, while others consider it a specific brainstem nucleus.  An example of the fact that little is actually clear-cut in the brain.


Limbic Core Networks

From the midbrain, a major reticular branch projects into the hypothalamus, as described earlier.  From there it projects throughout the limbic system.

Basal Forebrain and Substantia Innominata  –  The basal forebrain forms the base of the limbic system.  It’s a poorly defined region, directly above and in front of  the hypothalamus, with which it’s highly connected.

Substantia innominata  (“unnamed substance”) refers to reticular networks found prominently throughout the basal forebrain.  It also contains the reticular roots of all major systems within the limbic region.  In some places, those neural roots blend indistinguishably with substantia innominata networks.

Ascending reticular projections from hypothalamus make connections in substantia innominata, as they pass through on their way to other limbic regions.  The hypothalamus and substantia innominata function together as the limbic system’s reticular core.

Nucleus Basalis (or basal nucleus of Meynart, nucleus basalis magnocellularis)  –  not a single anatomical nucleus, but many noticeable clusters of very large neurons scattered throughout the substantia innominata.  The clusters are loosely interconnected and function loosely together as one network.

That network projects widely throughout the limbic system, then to parts of  cerebral cortex. Plays activating role in focused attention functions.  Acetylcholine is its main neurotransmitter.

And again, substantia innominata contains the intertwined roots of all major systems in the limbic region  –

 Centromedial Amygdala  –  the reticular core of the amygdala, located in the substantia innominata of the basal forebrain.

The amygdala itself has become well-known as the limbic system’s negative emotional processing center.  It underlies social anxiety and aggression, territorial competition and power/status drives.  And it underlies the depressive pain of social separation and loss.

The amygdala does also process some positive emotion.  And it plays a role in emotional learning, loosely described as “a kind of primitive emotional memory.”  But almost all agree that its overriding function is negative social emotions.

The centromedial amygdala is its oldest part.  It’s located in the reticular substantia innominata, and in some places blends with it.  It’s considered part of the reticular system, while other more specifically organized amygdala regions are not.

In recent decades the “extended amygdala” idea has gained traction.  It mostly involves the stria terminalis  –

Stria Terminalis (or nucleus stria terminalis)  –  a bundle of negative emotion network/pathways, projecting down from centromedial amygdala, making connections in substantia innominata, and passing through to connect with hypothalamus.

Some propose it should be considered part of the amygdala, a sort of deep connecting root or “extended amygdala.”  Either way, it’s a major reticular conduit, connecting negative emotion systems on brainstem and limbic levels.  It connects reptilian fight-flight programs with more complex, but basically similar, mammalian versions.

Nucleus Accumbens  –  located in substantia innominata of basal forebrain.   A key node in the brain’s pleasure-reward networks.  Important in the anticipatory reward (or SEEKING) system described earlier.  Plays lesser roles in fear processing and sleep regulation.

Septum (or septal region)  –  another important part of the limbic pleasure-reward system.  Located near nucleus accumbens, highly connected with it.

Activates social pleasures  –  loving and liking, sharing, playing, belonging, cooperating.     Central to parental emotions, family bonding, and altruism.  It’s the old mammalian source of positive human values.

Medial Forebrain Bundle  –  major reticular network/pathway interconnecting pleasure-reward systems.

Arises in midbrain ventral tegmental area (described above).  Projects upward into hypothalamus, connecting with positive nuclei/networks there.  Then projects into substantia innominata, making connections there, as it passes through to nucleus accumbens, septum, and other basal forebrain pleasure centers.  Sometimes referred to as a “river of reward.”

Ventral Pallidum  –  diffuse root system of the basal ganglia.

Basal ganglia are large  motor nuclei of the limbic region.  Most prominent are caudate, putamen, and globus pallidus.  Not usually classified as part of the limbic system, but occupy the same brain region and function closely with it.  Important in the behavioral expression of limbic emotions, including animals’ social signals and human “body language.”  Also connected with cerebral cortex, have poorly understood influences on cognitive functions.

Ventral pallidum is the largest reticular division of the basal ganglia.  It extends deep into the basal forebrain’s substantia innominata, where its networks intertwine with those of other systems in the limbic region.

Hippocampus  –  is actually the oldest part of the cerebral cortex.  A primitive version is even present in reptiles.  But is located in the limbic region, tied in with limbic circuits, and usually considered part of the limbic system.

Its reticular activation comes from both hypothalamic and thalamic branches of the core.

Plays key role in memory and learning.  Essential for systematic exploration of the environment, making mental maps, and navigating within the environment.

First constructs those maps in its own short-term memory circuits.  Then gradually transfers or consolidates them into long-term memory patterns in newer cortical areas.

In all mammals, it makes maps of the physical environment.  In humans, research strongly suggests that it also maps more abstract forms of knowledge.  It’s connected with all cortical areas, and plays a key role in “the computation of relationships among perceived, conceived, or imagined items.”

“The hippocampus, as the brain’s search engine also allows a fast and efficient search among the deposited memories in the neocortex, which is a process essential for planning the future…[It] appears that neural algorithms, perhaps evolved initially for computing first-order (neighborhood) and higher order (e.g., short-cuts, detours) distances in the physical world, are the same as those used for the navigation in cognitive space during recall and planning.”

                                                                                                                                         – Neurophysiologist Gyorgy Buzsaki

Limbic Cortex  –  Dr. Buzsaki adds  “nearly all hippocampal functions are performed in collaboration with several of its partners.”  Those hippocampal partners are other old cortical areas, located nearby and loosely labeled “limbic cortex.”  They work together with the hippocampus in exploration, navigation, map-making, and consolidating those maps into long-term memory.

Limbic cortex also works together with other limbic regions in their various, previously described, social-emotional functions.

For anyone interested, an internet search of these limbic cortical areas may help flesh out the overview  –  parahippocampal gyrus, entorhinal cortex, cingulate cortex, insular cortex, and medial prefrontal cortex.

Most limbic cortical areas are activated by both hypothalamic and thalamic branches of the reticular core.

Olfactory Pathways  –  underlie the sense of smell, the only sensory input not processed initially in the brainstem.  Olfaction is most mammals’ dominant sense, closely tied in with limbic functions, including social emotions and territorial mapping.  In humans, olfaction’s role has dwindled, but some fragrances or odors still evoke strong positive or negative emotions.

Olfactory pathways, like other limbic pathways, are rooted in and activated by substantia innominata.


In summary, the basal forebrain’s substantia innominata is an upward extension of midbrain and hypothalamic reticular networks.  Within it are the intertwined reticular roots of positive and negative social-emotion systems, basal ganglia, hippocampus, limbic cortex, and olfactory pathways.  The substantia innominata has been called “the centerpiece of this heterogeneous collection of anatomical systems.”  It and the hypothalamus function together as the limbic system’s core.


The TCS Core

The cerebral cortex is actually just the 1/8 inch surface layer of the two large cerebral hemispheres.  But the term is often used loosely, referring to the whole functional unit  –  the  thalamocortical system  (TCS)  –  thalamus, cerebral cortex, and their many connecting pathways.

The cortex is where most of the information processing occurs.  In humans it’s especially large, folded, and furrowed.  If spread out flat, an adult human cortex would cover about two and a half square feet, much larger than in any other animal.

Hippocampus and limbic cortex  (together = old cortex, described above) comprise about 10% of human cerebral cortex.  The rest is neocortex (new cortex), home of thinking and other cognitive functions.

As noted earlier, thalamus is important in perceptual processing.  Most of the brain’s sensory input  –  vision, hearing, touch, taste  –  is first processed in the lower brainstem, then relayed up to specific thalamic nuclei for further processing.  Here’s the highest level of perceptual processing in a reptile’s brain.

In humans, thalamus still processes perceptions, but also feeds those signals forward to sensory areas of the cerebral cortex.

Again, thalamus’ primary role is perceptual processing.  More than half of its approximately 60 specific nuclei process external sensory information.  But it also contains specific nuclei serving motor, visceral, and emotional functions.  Thalamus is a major intersection of pathways from many brain systems, and some  thalamic nuclei serve those other functions.

So thalamus has many functions, but our focus here is its core  –

 Zona Incerta (“zone of uncertainty”)  –  so named because little was known about it until recently.

An extension of midbrain reticular core into upper brainstem.  Located between midbrain and thalamus.   Interconnected with many brain regions, but projects most strongly to thalamic core nuclei.

 Midline and Intralaminar Nuclei  –  these are thalamic core nuclei, upward extensions of midbrain reticular core and zona incerta.  They are surrounded by specific thalamic nuclei, which they activate along with the cerebral cortex.

Matrix networks (or matrix cells)  –  many smaller reticular networks interlaced between, and even within, specific thalamic nuclei.  Strongly connected with midline and intralaminar nuclei.  Matrix networks also have activating influences throughout the TCS.

Midline, intralaminar, and matrix networks are often considered likely generators of core consciousness.  More on that shortly.

Specific thalamic nuclei (e.g., thalamic visual nuclei) project to relatively small, circumscribed cortical areas (e.g., certain parts of visual cortex).  In contrast, projections of core nuclei/networks are more diffuse and widespread.  Some project to larger, but still limited, cortical areas and probably serve focused attention functions.  Others project throughout the cortex and probably serve global awareness functions.  Much current research is directed toward clarifying their various, still mostly elusive, activation patterns.

Thalamic core networks project throughout the cerebral cortex, but projections to prefrontal cortex are particularly strong.  This underlies the role of prefrontal cortex as the emotional driver of other cortical areas (described in Essay 4).

Midline, intralaminar, and matrix nuclei/networks have mostly activating influences on the TCS.  But they function closely together with the inhibitory thalamic reticular nucleus

 Thalamic Reticular Nucleus  –  a net-like neural sheath around most of the thalamus, described earlier this essay.  It’s mostly inhibitory.  All signal traffic between thalamus and cortex must pass through this inhibitory filter.

Works together with activating core networks in many TCS functions.  Perhaps best-known are sleep-wake cycles and control of attention  –

In sleep, its inhibiting influence contributes to global TCS deactivation.  But of course it’s all very complicated  —  for example, recall the many lower brainstem core networks that also influence sleep-wake patterns.

In waking, thalamic reticular nucleus underlies the well-known inhibitory or “filtering function” of attention.  Attention’s selective “spotlight” is generated by midline and intralaminar nuclei in the thalamic core, while thalamic reticular nucleus filters out noise, blur, and distraction.  It sharpens the beam and promotes perceptual clarity.

Medial Prefrontal Cortex (or mPFC)  –  Prefrontal cortex itself was described in  Essay 4.  It’s the (mostly) new emotional part of the cerebral cortex, highly developed in humans.  Drives positive and negative thinking patterns in other cortical areas.

The mPFC is the oldest part of prefrontal cortex, part of the old limbic cortex.     It’s a strong driver of all old and new cortical areas.

The mPFC receives particularly strong input from the reticular system.  Both hypothalamic and thalamic branches of the core send large reticular projections to mPFC.  They converge in mPFC, then project to other prefrontal areas, which drive and direct the rest of the cortex.

Advanced brain imaging techniques now confirm what scientists long suspected  —  mPFC plays a central role in cognition of the self.  The mPFC is where cognitive self-awareness (self-image, self-concept) begins.

Research on mPFC and “self-related processing” has been intense in recent years.  It’s advancing on many fronts, beginning to clarify the neural basis of self-other relations, self-reflection, positive and negative self-esteem, and so on.  Also starting to clarify which nearby limbic cortical areas function together with mPFC in which of its various self-related functions.

But our focus here is the brain’s core, in which mPFC and self-concept are rooted.  The reticular system is the functional and experiential core of mPFC and its cognitive self.  It’s at the center of the idea of “I”.  The mPFC has been called “the cortical entrance door to consciousness.”


This Glossary has traced core networks, from the lowest brainstem regions into the limbic system and cerebral cortex.  But which of those networks are most likely generators of core consciousness?


Generators of Core Consciousness

Among leading researchers, these get mentioned most often in that regard  —  thalamic core networks, hypothalamus, PAG, and core pleasure systems.

Thalamic core networks include midline and intralaminar nuclei, matrix networks, and zona incerta.  Their close relations with cerebral cortex make them seem likely generators of core consciousness, and research so far supports that.

Here are a few of those researchers and their conclusions:

Neurosurgeon Joseph Bogen, mentioned in Essay 1, concludes that thalamic intralaminar nuclei are the most likely generators of “a crucial core C”  –  pure subjective awareness or consciousness without content.

Meditation researchers often emphasize intralaminar and midline nuclei.  Among them is physiological psychologist Fred Travis, who includes thalamic matrix networks as well  –

“The ‘content’ of matrix circuits may be wakefulness itself.  Reverberations in matrix circuits do not encode perceptual features;  rather they encode fluctuations in waking or arousal levels… a dynamically changing continuum of wakefulness.”

Neuropsychologist Bjorn Merker, mentioned in Essay 1, studied the brainstem’s role in consciousness, including that of children born without a cerebral cortex.  He noted the zona incerta’s widespread connections, and its strong bridging role between midbrain core and thalamic core.  He concluded it may be “a midline straddling point of unity” and “the perfect anatomical centerpiece” for core consciousness.

Hypothalamus is sometimes considered a specialized part of the reticular system.  Others view it as an amalgamation of specific nuclei amidst reticular networks.  Either way, many view it as a likely contributor to core consciousness.  Among them are Damasio, Panksepp, and Merker.  And before them was neurophysiologist J.Z. Young  –  “the life promoting activities of the hypothalamus and reticular system,” he said,  “are at the centre of all consciousness.”

Periaqueductal gray  (PAG), located in the midbrain, is the lower brainstem region most often viewed as a source of core consciousness.  That includes Damasio, Panksepp, Merker, and many others.

PAG is an “emotional convergence zone” that brings together sensory, motor, and visceral inputs from many brain regions, organized in positive and negative networks.

Again, Panksepp called PAG “a Grand Central Station for our affective life…essential for the primal integration of diverse emotional experiences.  It extends its tentacles far into the lower and higher regions of the brain.”

Among PAG’s lower brainstem connections, Damasio emphasized solitary nucleus and parabrachial nucleus as also likely contributors to core consciousness.

Core pleasure systems are often assumed to be conscious. They include ventral tegmental area (midbrain), some PAG and hypothalamic nuclei/networks, medial forebrain bundle, nucleus accumbens, septum, and some substantia innominata networks.  All together they form a “river of reward.”

And through the reticular core itself flows a river of consciousness  —


River and Ocean

We don’t know which reticular networks actually generate core consciousness.   Probably many, or maybe most of them?

Through them flows an underground river of consciousness  —  a river of light, your sense of your soul.

And that river may merge with a universal ocean of consciousness.  Your individual soul may merge with the universal soul.

In Hinduism, Atman is an individual’s soul, and Brahman is the universal soul.  Atman and Brahman are one.

Similarly, modern physics suggests that consciousness is universal and undissectable  –  “the overall number of minds is just one.”  Our trouble understanding that is like an “optical illusion” or “delusion… a kind of prison for us.”

It’s nice to learn that our souls are probably not in solitary confinement, probably not awaiting death sentences.

But how does core consciousness connect with universal consciousness?  By what physical process might core brain energies resonate with quantum vacuum energy?

So far, science has little that’s clear or substantial to say about that.  Instead, the interface between neurophysiology and quantum physics is a hodgepodge of controversial theories, and limited data, as in any new interdisciplinary branch of science.  But one hint  —

A common thread throughout that literature is the notion of coherence  –  energy fields in synchrony or harmony, within themselves and with other fields.  It’s a key concept, obviously important, superficially easy to understand, but actually poorly understood in both quantum physics and neurophysiology.

Quantum coherence refers to the degree that a system exhibits various quantum properties (including some that seem impossible from a classical or commonsense perspective).  It’s a notoriously difficult concept, fully accessible only to physicists who understand its mathematical underpinnings.  But coherence and decoherence among energy fields is a central aspect of quantum physics.

Coherent brain rhythms were barely mentioned in previous essays, largely because they are so poorly understood.  There are several of these synchronous brainwave patterns, most prominently alpha, delta, theta, and gamma rhythms.  You can read about them  —  all fascinating, but also frustrating in our still poor basic understanding of them.

However, we do know that reticular networks play key roles in generating them all.  Other brain regions contribute to those rhythms, but none so much as the core.

And we know that those coherent brain rhythms are strongest during mindful prayer and meditation.  They are stronger in meditation than any other phase of sleep or waking.  The deeper the meditation, the stronger and more coherent those rhythms are.

So the field is full of speculations involving brain rhythms and/or quantum coherence, and their roles in consciousness and spiritual experience.  Again, it’s all tentative;  the field is in its infancy.

But mindful prayer and meditation do take you to your core.  They promote brainwave coherence.  They may also enhance your resonance with the universal force field.

Thanks for reading this.  May the Force be with you  —



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